The earliest maize from San Marcos Tehuacán is a partial domesticate with genomic evidence of inbreeding

Abstract

Pioneering archaeological expeditions lead by Richard MacNeish in the 1960s identified the valley of Tehuacán as an important center of early Mesoamerican agriculture, providing by far the widest collection of ancient crop remains, including maize. In 2012, a new exploration of San Marcos cave (Tehuacán, Mexico) yielded nonmanipulated maize specimens dating at a similar age of 5,300-4,970 calibrated y B.P. On the basis of shotgun sequencing and genomic comparisons to Balsas teosinte and modern maize, we show herein that the earliest maize from San Marcos cave was a partial domesticate diverging from the landraces and containing ancestral allelic variants that are absent from extant maize populations. Whereas some domestication loci, such as teosinte branched1 (tb1) and brittle endosperm2 (bt2), had already lost most of the nucleotide variability present in Balsas teosinte, others, such as teosinte glume architecture1 (tga1) and sugary1 (su1), conserved partial levels of nucleotide variability that are absent from extant maize. Genetic comparisons among three temporally convergent samples revealed that they were homozygous and identical by descent across their genome. Our results indicate that the earliest maize from San Marcos was already inbred, opening the possibility for Tehuacán maize cultivation evolving from reduced founder populations of isolated and perhaps self-pollinated individuals.maize | paleogenomics | teosinte | domestication | Tehuacán

A re‐evaluation of the domestication bottleneck from archaeogenomic evidence

“…Despite the physiological potential of a 5% inbreeding rate, the levels of inbreeding observed here have largely been observed in the field presumably due to such confounding factors (Sanvido et al., ). Previous studies have similarly hinted that maize may not outcross as frequently as is generally assumed (Bannert & Stamp, ), and evidence of extreme inbreeding has been observed directly in ancient maize genomes (Vallebueno‐Estrada et al., ).…”

Stepwise cis-Regulatory Changes in ZCN8 Contribute to Maize Flowering-Time Adaptation

“…A total of 19 archaeological maize samples were sequenced in the three studies, including four 5000-year-old maize specimens from the Tehuacan Valley[46, 47] and fifteen 1900-year-old maize cobs from Turkey Pen Shelter in the southwestern United States[48]. The read processing and mapping followed the previous studies[46–48]. Filtered reads were mapped to the maize reference genome AGPv3.29[63] using bwa mem v0.7.10[64].…”

Domestication as a model system for the extended evolutionary synthesis

“…Advances in the analysis of DNA extracted from archaeobiological remains and the ability to precisely date these remains, moreover, provide excellent opportunities to monitor the interplay among these developmental processes and manifestations of heritable genetic changes in emergent domesticates. Recent studies of ancient DNA extracted from ancient maize, for example, have made it possible to track the appearance of specific domestication genes in this important crop plant as it moved from the heartland of initial domestication in southwestern Mexico up through central Mexico and into the southwestern USA [94,140,141]. Another recent study of ancient DNA extracted from horse skeletal remains finds evidence of enrichment for genes involved in androgen and steroid hormone receptor binding indicative of the selective pressures for behavioural and cognitive changes central to animal domestication [142].…”